Ensembl Courses and Workshops

1
Exercises BIOMART Exercises 1 - 4
2
The Ensembl Genebuild
3
Outline

• Ensembl gene set
• EST genes ab initio predictions
• Manual annotation (Vega / Havana)
• Ensembl / Havana merged gene set
• CCDS project

4
Biological Evidence
All Ensembl gene predictions are based on
experimental evidence

• UniProt/Swiss-Prot
• A manually curated database and therefore of
  highest accuracy
• NCBI RefSeq
• A partially manually curated database
• UniProt/TrEMBL
• Automatically annotated translations of EMBL
  coding sequence (CDS) features
• EMBL / GenBank / DDBJ
• Primary nucleotide sequence repository

5
The Ensembl Genebuild
Genome assembly

Experimental evidence
Ensembl Genes

Computer programs
6
Genome Assemblies

• Genome assemblies are not created by
• Ensembl, but provided by other institutes /
• consortia
• NCBI human, mouse
• Rat Genome Sequencing Consortium rat
• Sanger zebrafish
• Broad Institute mammals
• Baylor College cow
• Washington University chicken
• etc. etc.

7
The Ensembl Genebuild
A new release of Ensembl doesnt contain a new
genebuild for each species! New genebuilds are
only done if there is

• a new genome assembly
• a lot of new supporting evidence
• an improved genebuild procedure

8
The Ensembl Genebuild

• Every genome presents a unique challenge
• Amount and type of data available
• Existence of gene sets for evolutionary close
  species
• Availability of manually annotated gene sets